Prime Minister Tony Abbott has told the Egyptian president that detained Australian journalist Peter Greste was simply doing his job, while also expressing sympathy for the strife-torn country as it grapples with the Muslim Brotherhood.

Greste, a reporter with the Al Jazeera television network, was arrested in Cairo on December 29 along with two colleagues with the trio accused of spreading false news and supporting the black-listed group.

Mr Abbott on Saturday revealed details of his call to interim Egyptian President Adly Mansour on Thursday night, saying he had conveyed that he had a lot of sympathy with the Egyptian government and that in Australia's view, the Muslim Brotherhood was linked to terrorism.

"Second point I made was at least from this distance, Peter Greste was doing his job," he said.

"He wasn't taking sides.

"He was simply doing his job and it is the job of a free media to report the facts as they find them and that is what he was doing."

Mr Abbott said the president conceded he couldn't interfere in his country's justice process but was confident the matter would be resolved swiftly.